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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PERIPHERAL MYELIN PROTEIN 2
 
Authors :  E. Ugochukwu, E. Pilka, C. Phillips, W. W. Yue, T. Krojer, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, K. L. Kavanagh, U. Oppermann, Structural Genomics Consortium (Sgc)
Date :  30 Jun 10  (Deposition) - 04 Aug 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ugochukwu, E. Pilka, C. Phillips, W. W. Yue, T. Krojer, F. Von Delft C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, K. L. Kavanagh, U. Oppermann
Crystal Structure Of Human Peripheral Myelin Protein 2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PMP2 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-132
    Gene: HCG_21300, PMP2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PERIPHERAL MYELIN PROTEIN 2, CDNA, FLJ92018, HOMO SAPIENS PERIPHERAL MYELIN PROTEIN 2 (PMP2), MRNA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL1Ligand/IonCHLORIDE ION
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4GOL1Ligand/IonGLYCEROL
5PLM1Ligand/IonPALMITIC ACID
6SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:21 , GLY A:34 , ASP A:77 , ARG A:107 , ARG A:127 , TYR A:129 , HOH A:151 , HOH A:157BINDING SITE FOR RESIDUE PLM A 901
2AC2SOFTWARETRP A:98 , ASP A:99 , HOH A:227BINDING SITE FOR RESIDUE SO4 A 902
3AC3SOFTWAREALA A:37 , LYS A:38 , SER A:56 , THR A:57 , HOH A:162BINDING SITE FOR RESIDUE SO4 A 903
4AC4SOFTWAREASN A:16 , ASP A:19 , LYS A:80 , VAL A:123 , HOH A:199BINDING SITE FOR RESIDUE SO4 A 904
5AC5SOFTWARESER A:14 , ASN A:16 , PHE A:17 , ASP A:18 , HOH A:134 , HOH A:146BINDING SITE FOR RESIDUE GOL A 905
6AC6SOFTWAREARG A:53 , ASN A:60 , HOH A:243BINDING SITE FOR RESIDUE CIT A 906
7AC7SOFTWAREVAL A:12 , SER A:13 , GLY A:27 , LEU A:28 , ALA A:29 , ARG A:31 , HOH A:135 , HOH A:165BINDING SITE FOR RESIDUE EPE A 907
8AC8SOFTWAREGLY A:47BINDING SITE FOR RESIDUE CL A 908

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NR3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NR3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NR3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FABPPS00214 Cytosolic fatty-acid binding proteins signature.MYP2_HUMAN7-24  1A:7-24

(-) Exons   (0, 0)

(no "Exon" information available for 3NR3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:135
 aligned with MYP2_HUMAN | P02689 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:135
                               1                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127     
           MYP2_HUMAN     - ---MSNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFKLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 132
               SCOP domains d3nr3a_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeeeehhhhhhhhhh.hhhhhhhhhhh..eeeeeee..eeeeeee.....eeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FABP  PDB: A:7-24 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nr3 A  -2 YFQSMNKFLGTWKLVSSENFDDYMKALGVGLATRKLGNLAKPTVIISKKGDIITIRTESTFKNTEISFKLGQEFEETTADNRKTKSIVTLQRGSLNQVQRWDGKETTIKRKLVNGKMVAECKMKGVVCTRIYEKV 132
                                     7        17        27        37        47        57        67        77        87        97       107       117       127
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NR3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NR3)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MYP2_HUMAN | P02689)
molecular function
    GO:0015485    cholesterol binding    Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0005504    fatty acid binding    Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0061024    membrane organization    A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MYP2_HUMAN | P02689: 2wut 4a1h 4a1y 4a8z 4bvm 4d6a 4d6b

(-) Related Entries Specified in the PDB File

1pmp CRYSTALLOGRAPHIC STUDIES ON A FAMILY OF CELLULAR LIPOPHILIC TRANSPORT PROTEINS. REFINEMENT OF P2 MYELIN PROTEIN AND THE STRUCTURE DETERMINATION AND REFINEMENT OF CELLULAR RETINOL- BINDING PROTEIN IN COMPLEX WITH ALL-TRANS-RETINOL